[English] 日本語
Yorodumi
- PDB-5orf: Structure of ovine serum albumin in P1 space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5orf
TitleStructure of ovine serum albumin in P1 space group
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / ovine serum albumin / triclinic system
Function / homology
Function and homology information


enterobactin binding / lipid binding / extracellular space / metal ion binding
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin ...Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PROLINE / Albumin
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsTalaj, J.A. / Bujacz, A. / Bujacz, G. / Pietrzyk-Brzezinska, A.J.
Funding support Poland, 1items
OrganizationGrant numberCountry
NCN213/11/B/ST5/02271 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Crystal structures of serum albumins from domesticated ruminants and their complexes with 3,5-diiodosalicylic acid.
Authors: Bujacz, A. / Talaj, J.A. / Zielinski, K. / Pietrzyk-Brzezinska, A.J. / Neumann, P.
History
DepositionAug 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
C: Serum albumin
D: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,09123
Polymers265,7114
Non-polymers2,38019
Water6,972387
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1807
Polymers66,4281
Non-polymers7526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9235
Polymers66,4281
Non-polymers4964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1807
Polymers66,4281
Non-polymers7526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8084
Polymers66,4281
Non-polymers3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.820, 78.050, 109.710
Angle α, β, γ (deg.)89.81, 74.54, 73.15
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Serum albumin /


Mass: 66427.820 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Tissue: blood / References: UniProt: P14639
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.21 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2 M ammonium chloride, 0.1 M proline

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.07106 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2013 / Details: mirrors
RadiationMonochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07106 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 70636 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 3.64 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.36
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 7502 / % possible all: 87.5

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LUF
Resolution: 2.54→49 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 20.583 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25758 1414 2 %RANDOM
Rwork0.19563 ---
obs0.1969 69222 90.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.284 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å2-0.36 Å2-2.02 Å2
2---1.18 Å20.54 Å2
3----2.26 Å2
Refinement stepCycle: 1 / Resolution: 2.54→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18580 0 162 387 19129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01919188
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1191.97925916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30652328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88624.978892
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.726153476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4691588
X-RAY DIFFRACTIONr_chiral_restr0.1360.22839
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114324
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.64.2369357
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.8196.34111670
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6744.5289831
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.27835.89730799
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 99 -
Rwork0.269 4830 -
obs--84.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4997-0.14720.09620.42520.48690.71670.02450.1368-0.0315-0.12990.0999-0.0941-0.16170.2202-0.12440.0694-0.0040.0190.1465-0.0170.147674.926927.02542.6956
21.16930.49420.26660.92340.8810.88880.03890.0472-0.02980.0035-0.08260.0523-0.0131-0.07220.04370.11850.0223-0.01350.0694-0.00540.068155.262221.069837.0062
30.54890.29620.1621.47140.09890.05030.1169-0.0802-0.02370.0523-0.09040.00090.0394-0.022-0.02650.06220.0222-0.01370.0680.00380.130350.261518.885846.2185
40.4901-0.14740.26150.15960.11941.0018-0.00240.0356-0.02430.0424-0.0422-0.02290.00760.10330.04460.0872-0.01120.02750.08220.00930.123159.78933.915363.6382
52.2405-0.4307-1.86071.38870.76612.7676-0.04540.0316-0.01210.1924-0.0032-0.0480.190.0010.04870.10770.0162-0.00570.00950.02410.104258.426119.392265.2823
61.89442.3185-0.24334.1011-0.67790.91570.0297-0.05120.03650.2234-0.0884-0.11470.1312-0.05280.05870.08150.0023-0.00050.1110.03560.099551.222641.294980.2961
70.2018-0.06420.13082.09110.89170.7702-0.05260.02280.1302-0.0849-0.09730.26090.0639-0.09680.14980.0936-0.0165-0.05060.1462-0.00780.171446.810747.870673.42
80.88950.76461.97680.79741.69594.43260.0364-0.19260.0840.0573-0.15420.11440.1331-0.42750.11780.04590.0007-0.01050.207-0.06810.156434.230842.84464.638
92.28293.5089-1.10025.5836-1.08372.49670.14320.03820.01780.21960.0114-0.0058-0.1291-0.0643-0.15460.01510.0261-0.00230.172-0.02960.169735.566843.674642.7652
100.11890.20480.1390.8254-0.6212.01550.0575-0.0202-0.0440.1021-0.0651-0.1170.0729-0.1690.00760.08670.00370.00560.12620.00720.105442.969437.734549.4629
110.1581-0.2058-0.26492.9101-1.38642.7244-0.0832-0.06930.03950.02960.1126-0.2195-0.2012-0.2592-0.02940.13510.11460.00430.1494-0.00950.126144.425752.109750.2041
121.24431.27910.45612.62281.36140.78690.0020.07590.1751-0.0698-0.01870.0502-0.0471-0.09340.01660.0880.03520.00670.1582-0.03110.09335.871841.755929.4712
131.168-0.8187-0.46053.10071.22231.6221-0.032-0.02980.1108-0.06780.02130.1448-0.0777-0.20370.01070.01520.03350.00180.1201-0.00840.128525.87340.948824.8287
140.5915-0.30110.16550.60890.64411.21630.0347-0.0637-0.00340.10530.093-0.09590.20390.0561-0.12760.06540.04290.02360.1013-0.02170.156855.02860.02234.5058
151.50911.31190.10292.08861.00630.89590.089-0.2094-0.0890.1457-0.0764-0.07990.07570.1005-0.01260.0573-0.0029-0.00060.11110.02570.107647.558814.72717.2937
160.20380.04350.42770.13760.43251.8263-0.0403-0.01520.0164-0.04360.0520.0015-0.20640.0926-0.01170.05590.0050.06070.109-0.01390.12740.875720.480411.1644
170.51830.06390.52880.896-0.23361.71920.01610.1262-0.0922-0.22610.03350.04160.18840.0681-0.04960.0771-0.00060.01780.0968-0.00070.110330.82585.3557-5.657
182.10450.10660.24511.2948-0.02781.623-0.07350.20420.0996-0.17180.0108-0.073-0.12950.13880.06260.1103-0.02390.02780.08330.01820.060236.888218.337-8.9536
190.50130.8092-0.46291.3426-0.89261.4827-0.10530.03040.0022-0.1123-0.0075-0.0332-0.07540.01840.11280.07320.0086-0.01620.1090.01390.10812.24726.3836-14.4829
200.43540.44950.78011.30111.07851.70220.0515-0.08190.02640.0771-0.13850.15870.1063-0.1090.08710.02470.01650.02180.1167-0.02780.12159.39212.2522-5.5481
210.0982-0.0025-0.21170.1353-0.05180.4853-0.01540.1047-0.0507-0.0076-0.09730.02160.0144-0.19420.11270.05690.03010.00130.197-0.05640.15948.091412.14856.9641
221.60871.43891.29934.6863-0.64022.0078-0.0093-0.19250.0511-0.00020.07420.2456-0.0006-0.2745-0.06490.04120.02550.04880.11470.00090.102518.99638.057724.9928
230.3447-0.17150.38671.5207-0.19220.44170.0015-0.0805-0.0105-0.1174-0.00680.07490.0236-0.07820.00530.05310.00510.03310.08640.01860.11224.28569.637814.765
240.44920.1069-0.10911.5761-0.66540.2977-0.0540.1578-0.1362-0.11430.0389-0.04460.063-0.06760.01510.0825-0.0352-0.02070.1346-0.01260.154416.5762-2.718716.1422
250.64770.53140.22740.59640.46320.65230.1816-0.05470.17110.1572-0.09660.12530.0325-0.0454-0.0850.127-0.02390.04030.1127-0.01710.171326.18247.531836.2242
261.58671.00110.86231.49581.42351.3711-0.012-0.20610.11620.177-0.03540.06490.1574-0.01170.04740.1287-0.0360.0320.1747-0.01210.090221.677713.275644.252
270.42630.2499-0.06250.1732-0.11970.47450.0010.05270.05930.00490.04860.08350.0537-0.1623-0.04960.0540.01130.04340.0992-0.00070.160164.029638.2105102.7791
280.63660.1246-0.0240.03030.04630.70230.05030.08430.01180.0054-0.0050.0117-0.0577-0.0793-0.04530.08710.03780.03430.07940.0080.113378.201246.410989.8449
290.39260.25610.07881.1529-0.21990.86430.0299-0.04230.00370.0609-0.0808-0.0933-0.10270.01270.05090.07080.03390.05150.07650.0020.124987.051547.615595.8477
300.8266-0.4050.17820.3729-0.11440.58860.0496-0.06610.03370.0555-0.0678-0.00520.0846-0.06980.01820.1047-0.02770.02660.09580.02640.106787.322829.5428112.8201
310.5910.05170.36731.0634-0.17030.7741-0.18020.00490.11760.06340.1073-0.0699-0.173-0.02070.07290.13-0.0005-0.01340.0558-0.02890.089289.334943.7326116.0826
320.34820.32590.48621.74280.44351.3017-0.0878-0.12760.00570.02050.0362-0.034-0.04730.00880.05160.05160.0480.00510.13920.03250.1219103.002320.3362121.614
330.246-0.527-0.14372.9015-1.40872.1332-0.03940.0039-0.028-0.1820.0014-0.14010.1631-0.08890.0380.07190.02210.03030.10.04570.1672102.881615.2533112.773
340.086-0.44910.52883.0643-3.15314.1608-0.03990.01170.00950.0055-0.1777-0.222-0.00920.12920.21750.04880.02260.03630.15930.06690.1496109.777622.308399.9843
350.88041.350.94273.36410.03892.54710.1284-0.0931-0.06920.1611-0.1473-0.18590.1351-0.10930.01890.06630.03680.02080.0767-0.00130.110598.627624.851182.0283
360.6506-0.2126-0.00950.2615-0.38250.8741-0.01940.03360.0494-0.0067-0.0477-0.01610.0064-0.01070.06710.06490.02450.00830.0865-0.00580.119495.332929.183892.3114
370.61830.3054-0.76770.464-0.26920.9993-0.1001-0.0943-0.1189-0.0397-0.05750.04280.14190.11190.15750.11790.03940.00410.07870.00820.167994.636314.678790.994
380.34330.1544-0.18760.7666-1.00391.31550.00410.09380.0346-0.0544-0.0415-0.03390.07410.05120.03750.12310.02780.00040.0663-0.00580.093491.933628.428571.0098
391.4425-1.1214-0.04272.14150.00510.3309-0.02310.2120.1098-0.308-0.0411-0.12830.13470.1540.06420.13330.02620.040.13010.02360.097298.063930.918362.7443
401.1460.4642-0.59630.676-0.53120.48450.0838-0.09640.13470.2056-0.00170.0494-0.15310.0085-0.08210.11130.04060.0560.09570.00040.152261.717371.827564.7412
410.7742-0.2231-0.62090.22730.00360.6935-0.0167-0.08850.00360.07150.10990.0584-0.0695-0.0121-0.09320.05820.0010.00290.13240.02540.110274.671656.217370.4153
420.26310.17130.21740.33740.31930.32050.0072-0.00350.0130.02090.0391-0.07610.01450.011-0.04630.02410.00780.00410.11670.04710.15277.553951.588661.1492
430.70890.16640.24960.2837-0.20080.4132-0.0509-0.00070.1216-0.03990.02080.095-0.00550.01390.03010.0698-0.00350.01160.11180.02790.121678.053669.112743.6735
440.90280.2511-0.40391.4285-0.51710.516-0.07030.0355-0.0702-0.0866-0.00080.13630.1148-0.1560.0710.0589-0.02770.01210.1384-0.02060.127271.228156.283742.1598
450.6240.48330.24820.43590.4571.3752-0.1069-0.0040.0305-0.0756-0.07110.05210.03-0.15240.17810.09290.05050.03660.09460.0160.103689.493270.4327.1406
461.68031.8298-1.02052.2608-0.85341.3278-0.0055-0.1167-0.0085-0.0019-0.1647-0.1013-0.03940.12120.17010.04770.0482-0.01170.09650.07190.178396.623973.469134.0243
470.04950.10280.11150.27040.32660.41550.0060.0209-0.02320.01630.013-0.05440.0398-0.0214-0.01910.06440.05350.05110.18460.07430.1952104.152362.340342.812
480.18450.3569-0.62312.2041-0.98992.1440.0267-0.0329-0.0275-0.0488-0.1337-0.1612-0.06760.1180.1070.0474-0.0068-0.0050.10650.04970.1261103.597863.768764.3207
490.03740.19570.17421.40710.8510.86580.00370.00930.0184-0.0871-0.020.09420.04640.03910.01630.0737-0.00090.00580.08510.00710.125693.943562.8757.8057
500.00520.022-0.00870.41420.04280.0563-0.0176-0.00290.00130.0177-0.006-0.02010.03210.06750.02360.1007-0.0459-0.03020.17980.06730.1318101.203275.563656.9718
510.1318-0.2070.12440.384-0.43751.1172-0.062-0.04190.05670.1120.0543-0.0773-0.03610.04450.00770.0764-0.0153-0.0370.0930.02810.153102.840262.337477.5382
521.82080.895-0.50992.6259-0.98870.3964-0.0052-0.0084-0.14770.0346-0.0834-0.2412-0.00240.04360.08860.02580.0116-0.03860.08950.03020.1398110.515156.083181.6884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 106
2X-RAY DIFFRACTION2A107 - 147
3X-RAY DIFFRACTION3A148 - 198
4X-RAY DIFFRACTION4A199 - 250
5X-RAY DIFFRACTION5A251 - 295
6X-RAY DIFFRACTION6A296 - 336
7X-RAY DIFFRACTION7A337 - 366
8X-RAY DIFFRACTION8A367 - 398
9X-RAY DIFFRACTION9A399 - 417
10X-RAY DIFFRACTION10A418 - 468
11X-RAY DIFFRACTION11A469 - 497
12X-RAY DIFFRACTION12A498 - 537
13X-RAY DIFFRACTION13A538 - 583
14X-RAY DIFFRACTION14B1 - 106
15X-RAY DIFFRACTION15B107 - 147
16X-RAY DIFFRACTION16B148 - 198
17X-RAY DIFFRACTION17B199 - 250
18X-RAY DIFFRACTION18B251 - 295
19X-RAY DIFFRACTION19B296 - 336
20X-RAY DIFFRACTION20B337 - 366
21X-RAY DIFFRACTION21B367 - 398
22X-RAY DIFFRACTION22B399 - 417
23X-RAY DIFFRACTION23B418 - 468
24X-RAY DIFFRACTION24B469 - 497
25X-RAY DIFFRACTION25B498 - 537
26X-RAY DIFFRACTION26B538 - 583
27X-RAY DIFFRACTION27C1 - 106
28X-RAY DIFFRACTION28C107 - 147
29X-RAY DIFFRACTION29C148 - 198
30X-RAY DIFFRACTION30C199 - 250
31X-RAY DIFFRACTION31C251 - 295
32X-RAY DIFFRACTION32C296 - 336
33X-RAY DIFFRACTION33C337 - 366
34X-RAY DIFFRACTION34C367 - 398
35X-RAY DIFFRACTION35C399 - 417
36X-RAY DIFFRACTION36C418 - 468
37X-RAY DIFFRACTION37C469 - 497
38X-RAY DIFFRACTION38C498 - 537
39X-RAY DIFFRACTION39C538 - 583
40X-RAY DIFFRACTION40D1 - 106
41X-RAY DIFFRACTION41D107 - 147
42X-RAY DIFFRACTION42D148 - 198
43X-RAY DIFFRACTION43D199 - 250
44X-RAY DIFFRACTION44D251 - 295
45X-RAY DIFFRACTION45D296 - 336
46X-RAY DIFFRACTION46D337 - 366
47X-RAY DIFFRACTION47D367 - 398
48X-RAY DIFFRACTION48D399 - 417
49X-RAY DIFFRACTION49D418 - 468
50X-RAY DIFFRACTION50D469 - 497
51X-RAY DIFFRACTION51D498 - 537
52X-RAY DIFFRACTION52D538 - 583

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more